AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0369450


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTCTGGAATTTCTGAATT+TGG 0.187136 3_1:-66664409 Msa0369450:three_prime_UTR
TTGATATTGTTACATTGTTT+TGG 0.271278 3_1:-66664360 Msa0369450:three_prime_UTR
TGGATCTCTGTCTCATCTTT+CGG 0.332419 3_1:+66664659 None:intergenic
TGCTTCTGCGCAGTCTCATT+AGG 0.363924 3_1:-66664857 Msa0369450:five_prime_UTR
TGTAAAACAAACCATTTCAT+TGG 0.396362 3_1:+66664268 None:intergenic
AGTCCTAAAACCACAACAAT+TGG 0.396442 3_1:+66664323 None:intergenic
CACATCTTGTACCAATGAAA+TGG 0.407251 3_1:-66664279 Msa0369450:three_prime_UTR
GCGCAGAAGCAACTGCGATT+AGG 0.428523 3_1:+66664869 None:intergenic
CTTCGAGTGTTAGTCATGTT+AGG 0.446367 3_1:-66664302 Msa0369450:three_prime_UTR
AAGAACACCAACACACTACT+TGG 0.453868 3_1:+66664639 None:intergenic
AGCGTATGAGGAGGTTGAAG+AGG 0.488055 3_1:-66664687 Msa0369450:CDS
AGTGGAAGAAGAAGCGTATG+AGG 0.538884 3_1:-66664699 Msa0369450:CDS
TTCAACAATCATGCGTGCCA+AGG 0.540770 3_1:-66664807 Msa0369450:intron
GCACGCATGATTGTTGAAAA+CGG 0.548829 3_1:+66664812 None:intergenic
ATATGTTAAGAGAGTAGTAT+CGG 0.555824 3_1:-66664551 Msa0369450:three_prime_UTR
TTGTTGAAATCCAATTGTTG+TGG 0.563688 3_1:-66664333 Msa0369450:three_prime_UTR
CAGAGATCCAAGTAGTGTGT+TGG 0.590947 3_1:-66664646 Msa0369450:exon
AATATCAAAGATGAAAGCAT+AGG 0.592277 3_1:+66664375 None:intergenic
GGAAGAAGAAGCGTATGAGG+AGG 0.665498 3_1:-66664696 Msa0369450:CDS
ATAAGTCTGATTAAACAACA+CGG 0.774353 3_1:+66664578 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAACAAAAATTAATTGCAA+TGG + chr3_1:66664360-66664379 None:intergenic 15.0%
!!! TTTTGTTATAGTTATAATAG+TGG - chr3_1:66664376-66664395 Msa0369450:three_prime_UTR 15.0%
!!! TTTGATTTTGATTTTGATTT+TGG - chr3_1:66664405-66664424 Msa0369450:three_prime_UTR 15.0%
!!! TATAGTTATAATAGTGGTTT+TGG - chr3_1:66664382-66664401 Msa0369450:three_prime_UTR 20.0%
!!! CTCAAAGATATTTTTCTTTA+TGG - chr3_1:66664647-66664666 Msa0369450:exon 20.0%
!!! TTGATATTGTTACATTGTTT+TGG - chr3_1:66664775-66664794 Msa0369450:intron 20.0%
! ATAAGTCTGATTAAACAACA+CGG + chr3_1:66664560-66664579 None:intergenic 25.0%
! ATATGTTAAGAGAGTAGTAT+CGG - chr3_1:66664584-66664603 Msa0369450:three_prime_UTR 25.0%
!!! TTTTTTTGATTTTGCTGTTC+TGG - chr3_1:66664711-66664730 Msa0369450:intron 25.0%
!! AATATCAAAGATGAAAGCAT+AGG + chr3_1:66664763-66664782 None:intergenic 25.0%
!! TGTTCTGGAATTTCTGAATT+TGG - chr3_1:66664726-66664745 Msa0369450:intron 30.0%
!!! TATTGTTACATTGTTTTGGC+TGG - chr3_1:66664779-66664798 Msa0369450:intron 30.0%
TTGTTGAAATCCAATTGTTG+TGG - chr3_1:66664802-66664821 Msa0369450:intron 30.0%
! AATCCAATTGTTGTGGTTTT+AGG - chr3_1:66664809-66664828 Msa0369450:exon 30.0%
AATTGCAATGGATCTAACCT+TGG + chr3_1:66664348-66664367 None:intergenic 35.0%
! TTGATTTTGGATTTGTGCAG+TGG - chr3_1:66664418-66664437 Msa0369450:three_prime_UTR 35.0%
!! TCTCTCTCGTTTTGATGTTT+TGG - chr3_1:66664613-66664632 Msa0369450:three_prime_UTR 35.0%
AGTCCTAAAACCACAACAAT+TGG + chr3_1:66664815-66664834 None:intergenic 35.0%
CACATCTTGTACCAATGAAA+TGG - chr3_1:66664856-66664875 Msa0369450:five_prime_UTR 35.0%
GCACGCATGATTGTTGAAAA+CGG + chr3_1:66664326-66664345 None:intergenic 40.0%
TGGATCTCTGTCTCATCTTT+CGG + chr3_1:66664479-66664498 None:intergenic 40.0%
AAGAACACCAACACACTACT+TGG + chr3_1:66664499-66664518 None:intergenic 40.0%
CTTCGAGTGTTAGTCATGTT+AGG - chr3_1:66664833-66664852 Msa0369450:five_prime_UTR 40.0%
TTCAACAATCATGCGTGCCA+AGG - chr3_1:66664328-66664347 Msa0369450:three_prime_UTR 45.0%
! AGTGGAAGAAGAAGCGTATG+AGG - chr3_1:66664436-66664455 Msa0369450:three_prime_UTR 45.0%
CAGAGATCCAAGTAGTGTGT+TGG - chr3_1:66664489-66664508 Msa0369450:three_prime_UTR 45.0%
TGCTTCTGCGCAGTCTCATT+AGG - chr3_1:66664278-66664297 Msa0369450:three_prime_UTR 50.0%
! GGAAGAAGAAGCGTATGAGG+AGG - chr3_1:66664439-66664458 Msa0369450:three_prime_UTR 50.0%
AGCGTATGAGGAGGTTGAAG+AGG - chr3_1:66664448-66664467 Msa0369450:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 66664269 66664888 66664269 ID=Msa0369450;Name=Msa0369450
chr3_1 mRNA 66664269 66664888 66664269 ID=Msa0369450-mRNA-1;Parent=Msa0369450;Name=Msa0369450-mRNA-1;_AED=0.00;_eAED=0.00;_QI=69|1|1|1|1|1|2|385|25
chr3_1 exon 66664269 66664719 66664269 ID=Msa0369450-mRNA-1:exon:13593;Parent=Msa0369450-mRNA-1
chr3_1 exon 66664808 66664888 66664808 ID=Msa0369450-mRNA-1:exon:13592;Parent=Msa0369450-mRNA-1
chr3_1 five_prime_UTR 66664820 66664888 66664820 ID=Msa0369450-mRNA-1:five_prime_utr;Parent=Msa0369450-mRNA-1
chr3_1 CDS 66664808 66664819 66664808 ID=Msa0369450-mRNA-1:cds;Parent=Msa0369450-mRNA-1
chr3_1 CDS 66664654 66664719 66664654 ID=Msa0369450-mRNA-1:cds;Parent=Msa0369450-mRNA-1
chr3_1 three_prime_UTR 66664269 66664653 66664269 ID=Msa0369450-mRNA-1:three_prime_utr;Parent=Msa0369450-mRNA-1
Gene Sequence

>Msa0369450

ATGCGTGCCAAGTGGAAGAAGAAGCGTATGAGGAGGTTGAAGAGGAAGCGCCGAAAGATGAGACAGAGATCCAAGTAG

Protein sequence

>Msa0369450

MRAKWKKKRMRRLKRKRRKMRQRSK*